read.genepix {sma}R Documentation

Reading in Data Generated by the Image Analysis Package GenePix.

Description

Reads in a data file in table format and creates a data frame with the same number of rows as there are lines in the file, and the same number of columns as there are fields in the file.
`read.genepix' reads in the data file generated by the software "GenePix".

Usage

read.genepix(name, dir = ".", sep = "\t", header = TRUE, skip = 26, gpname = c("Block", "Col", "Row", "Name", "ID", "X","Y", "Dia", "Rmed", "Rmean", "RSD", "Rbmed", "Rbmean", "RbSD", "Rb1SD", "Rb2SD", "Rbsat","Gmed", "Gmean", "GSD", "Gbmed", "Gbmean", "GbSD", "Gb1SD", "Gb2SD", "Gbsat", "ratiomed", "ratiomean", "medratio", "meanratio", "ratiosd", "Rratio", "RegR2", "FPixels", "BPixels", "summed", "summean", "logratio", "Rmedc", "Gmedc", "Rmeanc", "Gmedc", "flags"),...) 

Arguments

name character string naming the data file from which to read the data.
dir character string naming the directory that contains the data file.
sep the field separator (single character), often "t" for tab delimited fields. If omitted, any amount of white space (blanks or tabs) can separate the fields. To read fixed format files, make sep a numeric vector giving the initial columns of the fields.
header logical flag: if TRUE, then the first line of the file is used as the variable names of the resulting data frame.
skip the number of lines of the data file to skip before beginning to read data.
gpname A vector of column names. SOme of the column names from genepix contain non standard characters, so useful to redefine to something R likes to use. Also newer versions of genepix have more columns
... parameters for read.table may also be supplied as arguments to the function (see read.table).

Value

as in read.table, a data frame (data.frame) containing a representation of the data in the file.

See Also

read.table, data.frame, read.spot.


[Package sma version 0.5.15 Index]